Kerala were 31-run ahead in their second innings with Nikhilesh Surendran (0 batting) and VA Jagadeesh (0 batting) in the middle when stumps were drawn for the day.
Niyas shone with six for 82 as Goa were bowled out for 242 in response to Kerala's first innings total of 273.
Earlier, Goa who resumed on 11 for no loss, lost opener Swapnil Asnodkar (13) to Niyas in the first session.
Other opener Amogh Sunil Desai (49) and Sagun Kamat (96) added 117 runs for the second wicket as Goa looked well on course to surpass Kerala's first innings score.
Kamat missed out on a well-deserved century by just four runs as he was caught by Surendram off Rohan Prem with the score on 162. His 155-ball knock was laced with 13 fours and a six.
None of the other batsmen offered any resistance and the side was dismissed for 242.
Apart from Niyas, Prem also accounted for two wickets.
Brief scores:
Kerala: 273 and 0/0 in 1 over
